title: mouse-acc

first: yanyong

last: cheng

address: 639 Zhizaoju Road

department: Department of Anesthesiology

institute: Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10&Mmul_10
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: nucleus

growth_protocol: The tissues samples of ACC and RSC were surgically removed and the frozen tissue was used to intact nucleus isolation. The nucleus was isolated and purified as previously described with some modifications

extract_protocol:
Sample washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA. Dissociated single cells were then stained with AO/PI for viability assessment using Countstar Fluorescence Cell Analyzer.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: without treatment

value: brain

tag: brain region

value: Anterior cingulate cortex (ACC)

tag: passage


title: Diabetic Foot Skin Donor #5 [DW5]

status: Public on May 30 2024

type: SRA

city: luzhou

last: Jiang

address: Zhong Shan Road

country: China

institute: SWMU

library_source: transcriptomic

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten / NovaSeq 6000 sequencer (2 × 150bp read length).
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2. The mapped reads of each sample were assembled by StringTie
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Diabetic foot skin

extract_protocol:
The total RNA was extracted from the tissue using TRIzol® Reagent according the standard procedure. RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: foot Skin

tag: disease

value: diabetes


title: Rhesus Macaque DHNC collected at d7

type: RNA

city: Salvador

first: Eduardo

last: Fukutani

state: Bahia

address: Marginal da - Av. Luís Viana Filho, 3230 - Imbuí, Salvador - BA

country: Brazil

institute: Fundação Oswaldo Cruz

hyb_protocol: Non applicable

scan_protocol: Digital mRNA gene expression analysis was performed with the Nanostring nCounter NHP Immunology panel V2 (Cat # 115000276).

data_processing: Raw read counts were obtained from RCC files using the nSolver 4.0 Data Analysis software and the NS_NHP_Immunology_V2.0 rlf file references included with the nCounter NHP Immunology panel V2 kit.

label: Non applicable

organism: Macaca mulatta

source_name: Cryopreserved Bronchoalveolar lavage (BAL) cells collected at days 0, 3, 7, 14 and 28-35 (necropsy) post-infection

label_protocol: Non applicable

extract_protocol: Cryopreserved BAL cells from pre-infection (d0) and days 3, 7, 14, and 28-35 post infection (necropsy) were thawed and homogenized using Qiagen RLT buffer Plus (Cat # 1053393) and QIAShredder Columns (Cat # 79656). RNA was isolated using the Qiagen RNeasy Mini kit (Cat # 74134) according to manufacturer’s instructions and eluted in 25uL of RNase free water. RNA was concentrated to 25-50ng/uL using Eppendorf Vacufuge plus centrifuge concentrator. RNA quality was confirmed with Agilent TapeStation. RNA was sent to the National Cancer Institute (NCI) Center for Cancer Research Genomics Core at the Frederick National Laboratory.

tag: animal id

value: DHNC

tag: time point

tag: treatment

value: control


title: K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep2, 1h

city: Göttingen

first: Kristina

last: Žumer

address: Am Faßberg 11

department: Department of Molecular Biology

country: Germany

institute: Max Planck Institute for Multidisciplinary Sciences

library_source: genomic

data_processing:
ChIP-seq reads were aligned to human hg38 genome assembly merged with D.melanogaster genome using Bowtie 2 with the following parameters: -p 24 --no-discordant --no-mixed --very-sensitive. Duplicates were removed using Picard tools.
Assembly: GRCh38
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: genome edited K562

growth_protocol: Cells were subcultured in RPMI medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 1x GlutaMax (Thermo Fisher Scientific) and maintained at densities between 1.5x105 and 7x105 cells/ml

extract_protocol:
Cells were fixed with 1% formaldehyde (Thermo Scientific) for 8 min. 125 mM Glycine was added to quench the reaction and incubated for 5 min. A pellet containing 30 million cells was lysed with 5 mL of Farnham lysis buffer (5 mM Pipes pH 8.0, 85 mM KCl, 0.5% NP-40, 1x protease inhibitor (Sigma-Aldrich), 1x phosphatase inhibitor (Sigma-Aldrich)) for 10 min on ice. Nuclei pellet was resuspended with 1 mL of sonication buffer (10 mM Tris-HCl pH 7.5, 1mM EDTA, 0.4% SDS, 1x protease inhibitor, 1x phosphatase inhibitor) and incubated on ice for 10 min. Chromatin shearing was done using S220 Focused-ultrasonicator (Covaris) with following settings: duty cycle 5%, peak incident power 140W, cycle per burst 200, processing time 900 sec, bath temperature 6 °C, degassing mode continuous, water level (Run) 8.
ChIP-seq DNA library preparation was performed according to NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 30 million cells per biological replicate were treated with dTAG7 or DMSO (control) for 1 h or 4 h.

tag: cell line

value: genome edited K562

tag: cell type

value: chronic myelogenous leukemia

tag: genotype

value: SSRP1 N-terminal dTAG

value: DMSO 1h

tag: chip antibody

value: Rpb1 NTD antibody (CST, #14958)


title: Rhesus Macaque DHNC collected at d3


title: dTAG_4hr_rep4

city: Goettingen

first: Abrar

last: Aljahani

address: Am Fassberg 11

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq550 output.
MCC pipeline (https://github.com/jojdavies/Micro-Capture-C)
ICE normalization (Imakaev et al. Nature Methods 2012)
Assembly: hg38
Supplementary files format and content: Chimeric junctions files: tab-delimited text files listing the locations of the identified valid junctions
Library strategy: Tiled-Micro-Capture-C (Tiled-MCC)

source_name: Bone Marrow

growth_protocol: RPMI-1640 (no glutamine), 10% fetal bovine serum, 1% GlutaMAX. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 2% formaldehyde for 10 minutes and permeabilised with 0.0025% digitonin. Chromatin was digested by MNase and religated. Decrosslinking and DNA extraction was performed. Samples were sonicated using a S220 focused-ultrasonicator (Covaris).
Tiled-Micro-Capture-C (Tiled-MCC) combines Micro-Capture-C (MCC) library preparation with oligonucleotide capture enrichment for deep, targeted sequencing of chromatin interactions within regions of interest. Details are described in the Methods section of the paper.

treatment_protocol: Cells were treated as described in the Methods section of the paper

value: Bone Marrow

value: Lymphoblast


title: Rhesus Macaque DHNC collected at d0


title: Diabetic Foot Skin Donor #4 [DW4]


title: dTAG_4hr_rep3


title: Diabetic Foot Skin Donor #3 [DW3]


title: monkey18-2-rsc

city: shanghai

value: Retro splenial cortex (RSC)


title: Rhesus Macaque DHDI collected at d28

value: DHDI


title: mouse-rsc

organism: Mus musculus


title: Diabetic Foot Skin Donor #2 [DW2]


title: Diabetic Foot Skin Donor #1 [DW1]


title: dTAG_4hr_rep1


title: Rhesus Macaque DHDI collected at d14


title: dTAG_4hr_rep5


title: monkey17-1-rsc


title: Covid_female_32245_1_B037_ATAC

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

country: USA

institute: Allen Institute

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger/cellranger-atac mkfastq (10x Genomics v.1.1.0).
10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes
Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.

tag: Sex

value: female

tag: visit

value: Visit 1


title: Rhesus Macaque DHDI collected at d3


title: DMSO_4hr_rep5

value: DMSO


title: monkey18-2-acc

value: brain

value: Anterior cingulate cortex (ACC)


title: Rhesus Macaque DHDI collected at d7


title: hybrids D. Melanogaster x D.simulans, ovaries, small RNA rep2

city: Moscow

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

country: Russia

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

library_source: other

data_processing:
For piRNA production analysis adapter sequences were removed by cutadapt 2.8. After quality control with FastQC rRNA, snRNA, snoRNA, and tRNA were filtered from libraries using bowtie (version 1.1.0) with -v 3 parameter. Unaligned reads were then filtered against microRNA set of D. simulans and D. melanogaster obtained from https://ftp.flybase.net/releases/current/dsim_r2.02/ and https://ftp.flybase.net/releases/current/dmel_r6.56/, resrespectively. Small piRNAs of 23–29 nt in length were selected using cutadapt 2.8. This piRNA fraction was mapped to Drosophila transposon canonical sequences v10.1 (https://github.com/bergmanlab/drosophila-transposons/) using bowtie version 1.1.0 with parameters -l 35 -n 3. Mapped reads were counted with htseq-count 2.0.0
Assembly: transposon canonical sequences v10.1 (https://github.com/bergmanlab/drosophila-transposons/)
Supplementary files format and content: piRNA counts for transposon canonical sequences obtained by  htseq-count 2.0.0

molecule: other

organism: Drosophila melanogaster x Drosophila simulans

source_name: ovaries

extract_protocol:
For small RNA libraries preparation RNA was extracted from 0-3 days old gonads of D. melanogaster Hmr2, D. simulans w501 and interspecific hybrids. Small RNA fraction (19-29 nt) was purified by 15% polyacrylamide gel from 20-30 μg total RNA.
Small RNA libraries were prepared using NEBNext Multiplex Small RNA Sample Prep Set for Illumina (#E7300S, NEB) and sequenced on NovaSeq 6000 in 100 bp single-end mode yielding 25-40 million single-end reads per library.

value: ovaries


title: Rhesus Macaque DHDI collected at d0


title: K562, SSRP1-dTAG, Pol II, ChIP, DMSO, rep2, 4h

value: DMSO 4h


title: DMSO_4hr_rep3


title: monkey18-1-acc


title: Rhesus Macaque DHMM collected at d28

value: DHMM

value: control


title: hybrids D. Melanogaster x D.simulans, ovaries, small RNA rep1


title: monkey18-1-rsc


title: dTAG_4hr_rep2


title: monkey17-2-acc


title: DMSO_4hr_rep2


title: monkey18-3-rsc


title: hybrids D. Melanogaster x D.simulans, ovaries, rep2

data_processing:
RNA-seq libraries of ovaries of hybrids and parental species were pseudo-aligned by kallisto v.0.50.0 (Bray et al., 2016) with following parameters: --single -l 100 -s 0.05. Merged transcriptome sets obtained from NCBI were used as reference (GCF_000001215.4 and GCF_016746395.2 assemblies for D. melanogaster and D. simulans, respectively). Quantified abundances of transcripts for protein-coding genes were imported with tximport v.1.24.0 (Soneson et al., 2015).
Assembly: GCF_000001215.4 and GCF_016746395.2 assemblies for D. melanogaster and D. simulans, respectively
Supplementary files format and content: Summarized transcript-level abundance, estimated counts and transcript lengths in csv format file

molecule: polyA RNA

extract_protocol:
For the preparation of RNA-seq libraries, RNA was isolated from D. melanogaster Hmr2, D. simulans w501 and interspecific hybrid ovaries with TRIzol Reagent (Invitrogen). PolyA selection was done using an Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific).
RNA-seq libraries were generated using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (#E7760, NEB) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, NEB #E7335, and Set 2, NEB #E7500) according to the manufacturer's instructions and sequenced on the Illumina NovaSeq 6000 SP platform (100 bp runs).


title: Rhesus Macaque DHMM collected at d7


title: DMSO_4hr_rep1


title: monkey17-1-acc


title: Rhesus Macaque DHMM collected at d3


title: hybrids D. Melanogaster x D.simulans, ovaries, rep1


title: DMSO_4hr_rep4


title: 3094647_Batf-Batf-2

status: Public on May 29 2024

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Trim_Galore(v0.4.4) is used to quality trim 3’ reads raw reads with the cutadapt (DOI: 10.14806/ej.17.1.200) program. A quality score cutoff of Q20 is used.
Trimmed reads are mapped to the mm10(Gencode GRCm38) reference genome by bwa(v0.7.12-r1039, PMID: 19451168) and converted to a bam file(a binary version of sam file) by samtools(v1.2, PMID: 19505943).
biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) was used to mark duplicated reads and non-duplicated reads were kept by samtools (parameter “-q 1 -F 1804” version 1.2).
All samples have more than 5 million fragments as suggested by CUT&RUN protocol paper. We generated bigwig files using the center 80 bp of fragments smaller than 2000 bp and normalized to 10 million fragments. We confirmed the replicability between replicates.
Assembly: mm10(Gencode GRCm38)
Supplementary files format and content: bigwig
Library strategy: Cut&Run

source_name: Spleen and lymph nodes

extract_protocol:
CD4 T cells were enriched by EasySep Mouse CD4 T Cell Isolation Kit (STEMCELL) from lymph nodes and spleens. naive T cells (CD4+GFP-CD44loCD62Lhi), Natural Treg cells (CD4+GFP+) T cells, resting Treg cells (rTreg: CD4+GFP+CD44loCD62Lhi), activated Treg cells (aTreg: CD4+ GFP+CD44hiCD62Llo) were further sorted by FACS.
Libraries were prepared with precipitated DNA using KAPA Hyper Prep Kit (Kapa Biosystems). The library DNA was enriched by size selection with AMPure XP beads.

value: Spleen and lymph nodes

tag: antibody

value: Anti-Batf

value: ex vivo cultured Th0 cells

value: Batf ectopic expression

value: anti-CD3/anti-CD28 restimulation


title: 3094645_Batf-WTBatf-2

value: Flag-Foxp3 and Batf ectopic expression


title: 3094644_Batf-WTBatf-1


title: monkey17-2-rsc

value: Retro splenial cortex (RSC)


title: 3094642_Flag-M4-1

value: Anti-Flag

value: Flag-Foxp3M4 ectopic expression


title: 3094646_Batf-Batf-1


title: 3094643_Flag-M4-2


title: 3094639_Flag-WT-2

value: Flag-Foxp3 ectopic expression


title: 3094638_Flag-WT-1


title: 2705183_Ets1_sgEts1_1

value: ex vivo cultured nTreg cells

value: sgEts1 in RosaCas9/+ Foxp3gfp


title: 3094635_Flag-WTBatf-2


title: Rhesus Macaque DHMM collected at d0


title: 2705182_Ets1_NC_2

value: sgNC in RosaCas9/+ Foxp3gfp


title: 2705184_Ets1_sgEts1_2


title: 2705180_Foxp3_sgEts1_2


title: 3094634_Flag-WTBatf-1


title: 2705181_Ets1_NC_1


title: 2693827_Foxp3_CsA_aTreg_2

value: Activated Treg (aTreg)

value: Cyclosporine (CsA)


title: 2693828_Foxp3_CsA_aTreg_3


title: 2693826_Foxp3_CsA_aTreg_1


title: 2705179_Foxp3_sgEts1_1


title: 2693824_Foxp3_Oil_aTreg_2

value: Oil


title: 2705177_Foxp3_NC_1


title: 2693823_Foxp3_Oil_aTreg_1


title: 2693825_Foxp3_Oil_aTreg_3


title: Kidney_KBU_2

city: Shanghai

first: Yutong

last: Hou

address: 227 South Chongqing Road

institute: SJTU

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp.
Trimmed sequence reads were mapped to GRCm38.102/hg38 or GRCh38.102/mm10 using Hisat2.
Read count extraction and normalization were performed using Stringtie.
Assembly: hg38; mm10
Supplementary files format and content: kidney_UUO_raw_counts.txt:  tab-delimited text file includes FPKM values and raw counts for each Sample (UUO set)

source_name: Kidney

extract_protocol:
RNA was harvested using TRNzol Universal Reagent (TIANGEN). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using mRNA-seq Lib Prep Kit for Illumina (ABclonal, China) following Sample Preparation Guide.

value: Kidney

value: Pcmt1 tKO

value: UUO+DMSO


title: Kidney_KLU_3


title: Kidney_KBU_1


title: Kidney_KLU_1


title: Kidney_KLU_2


title: Kidney_KBC_3

value: Sham+DMSO


title: Kidney_KBU_3


title: Kidney_KBC_1


title: Kidney_KBC_2


title: Kidney_WLU_4

value: Pcmt1 fl/fl


title: Kidney_WLU_3


title: Kidney_WLU_1


title: Kidney_WBU_2


title: Kidney_WBC_3


title: 2705178_Foxp3_NC_2

value: Spleen and lymph nodes

value: anti-CD3/anti-CD28 restimulation


title: Kidney_WBU_3


title: Kidney_WBC_1


title: Kidney_WBU_1


title: 1653_dKO4

city: Rochester

first: Isaac

middle: Spencer

last: Harris

state: New York

address: 601 Elmwood Ave

department: Department of Biomedical Genetics

institute: University of Rochester Medical Center

data_processing:
Demultiplexing, QC, Alignment, and Analysis
Raw reads generated from the Illumina basecalls were demultiplexed using bcl2fastq version 2.20.0. Quality filtering and adapter removal are performed using FastP version 0.23.1 with the following parameters:  "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r".1 Processed/cleaned reads were then mapped to the GRCm39/gencode M31 reference using STAR_2.7.9a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM Unsorted – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReadsUnmapped Fastx".2,3 Genelevel read quantification was derived using the subread-2.0.1 package (featureCounts) with a GTF annotation file (GRCm39/gencode M31) and the following parameters for stranded RNA libraries  "-s 2 -t exon -g gene_name" OR  "-s 0 -t exon -g gene_name" for un stranded libraries.4 Differential expression analysis was performed using DESeq2-1.34.0 with a P-value threshold of 0.05 within R version 3.5.1 (https://www.R-project.org/).5 A PCAplot was created within R using the pcaExplorer to measure sample expression variance.6 Heatmaps were generated using the pheatmap package were given the rLog transformed expression values.7 Gene ontology analyses were performed using the EnrichR package.8,9,10 Volcano plots and dot plots were created using ggplot2.11
References
1: Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560
2: Frankish A, Diekhans M, Jungreis I, et al. GENCODE 2021. Nucleic Acids Res. 2021;49(D1):D916-D923. doi:10.1093/nar/gkaa1087
3: Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635
4: Liao Y, Smyth GK, Shi W (2019). “The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads.” Nucleic Acids Research, 47, e47. doi: 10.1093/nar/gkz114.
5: Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8.
6: Marini F, Binder H (2019). “pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components.” BMC Bioinformatics, 20(1), 331. doi: 10.1186/s12859-019-2879-1, https://bioconductor.org/packages/pcaExplorer/.
7: Kolde, Raivo. Package ‘pheatmap’. Version 1.0.12. https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf
8: Chen EY, Tan CM, Kou Y, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14:128. Published 2013 Apr 15. doi:10.1186/1471-2105-14-128
9: Kuleshov MV, Jones MR, Rouillard AD, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44(W1):W90-W97. doi:10.1093/nar/gkw377
10: Xie Z, Bailey A, Kuleshov MV, et al. Gene Set Knowledge Discovery with Enrichr. Curr Protoc. 2021;1(3):e90. doi:10.1002/cpz1.90
11: Wickham H (2016). ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York. ISBN 978-3-319-24277-4, https://ggplot2.tidyverse.org.
Assembly: Genecode M31
Supplementary files format and content: Excel file with normalized rlog transformed counts.

source_name: Liver

extract_protocol:
Tissue samples were crushed on dry ice and homogenized using a bead Mill (VWR). mRNA was then isolated from the tissues using E.Z.N.A. total RNA Kit I (Omega Bio-Tek, R6834-02).
RNA libraries for RNA-seq were prepared using Illumina Stranded mRNA Prep Kit following manufacturers protocols.

value: Liver

value: DKO


title: 1657_dKO2


title: 1656_dKO1


title: 1652_dKO3


title: 1696_Nrf2_KO4

value: Nrf2 KO


title: 1604_Nrf2_KO3


title: 1672_Gclc_KO4

value: Gclc KO


title: 1697_Nrf2_KO1


title: 1708_WT1

value: WT


title: 1682_WT4


title: 1679_WT3


title: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 3_ATAC

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

department: Pathology and Immunology

institute: Washington University School of Medicine in St. Louis

description: scATAC Seq: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 3

library_source: genomic single cell

data_processing:
Paired scRNAseq/scATACseq data produced from Chromium Single Cell Multiome ATAC + Gene Expression was processed using the cellranger-arc count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix folder contents produced by the CellRanger pipelines, containing three files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz. For the multiome samples, we also have deposited atac_fragments.tsv.gz and atac_fragments.tsv.gz.tbi files.

source_name: BM

extract_protocol:
As described in Material and Methods
Please refer to Method section of the manuscript
ScMultiome protocol (10x), refer to Method section of the manuscript for further information

value: BM

value: Lin-B220-Flt3+ BM progenitors

value: CD300ciCre-hCD2/WT R26tdTomato/WT

value: No treatment

tag: library type

value: ATAC

tag: hto


title: 1668_Gclc_KO3


title: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 3_RNA

description: scRNA Seq: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 3

library_source: transcriptomic single cell

value: RNA


title: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 1_ATAC

description: scATAC Seq: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 1


title: 1688_Gclc_KO2


title: CD11c+ splenocytes derived from Ms4a3 Cre R26tdTomato mice_HTO

description:
HTO
Ms4a3_barcodes.tsv.gz
Ms4a3_features.tsv.gz
Ms4a3_matrix.mtx.gz

data_processing:
3' scRNAseq data was processed using the cellranger count pipeline (CellRanger version 7.1.0, 10X Genomics) with default settings.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix folder contents produced by the CellRanger pipelines, containing three files per sample: barcodes.tsv.gz,  features.tsv.gz and matrix.mtx.gz.

molecule: protein

source_name: Spleen

extract_protocol:
As described in Material and Methods
Please refer to Method section of the manuscript

value: Spleen

value: CD11c+ splenocytes

value: Ms4a3-Cre/WT R26tdTomato/WT

value: HTO

value: TotalSeq™-B0301 anti-mouse Hashtag 1 Antibody, TotalSeq™-B0302 anti-mouse Hashtag 2 Antibody and TotalSeq™-B0303 anti-mouse Hashtag 3 Antibody


title: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 2_ATAC

description: scATAC Seq: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 2


title: 1709_WT2


title: CD11c+ splenocytes derived from IL-7R Cre R26tdTomato mice_HTO

description:
HTO
IL-7R_barcodes.tsv.gz
IL-7R_features.tsv.gz
IL-7R_matrix.mtx.gz

value: IL-7R-Cre/WT R26tdTomato/WT


title: CD11c+ splenocytes derived from Ms4a3 Cre R26tdTomato mice_RNA

description:
polyA RNA
Ms4a3_barcodes.tsv.gz
Ms4a3_features.tsv.gz
Ms4a3_matrix.mtx.gz


title: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 2_RNA

description: scRNA Seq: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 2


title: CD11c+ splenocytes derived from IL-7R Cre R26tdTomato mice_RNA

description:
polyA RNA
IL-7R_barcodes.tsv.gz
IL-7R_features.tsv.gz
IL-7R_matrix.mtx.gz


title: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 1_RNA

description: scRNA Seq: BM progenitors derived from CD300ciCre-hCD2 R26tdTomato mouse number 1


title: CD11c+ splenocytes derived from CD300ciCre-hCD2 R26tdTomato mice_HTO

description:
HTO
CD300c_barcodes.tsv.gz
CD300c_features.tsv.gz
CD300c_matrix.mtx.gz


title: Muscle, Icos-/- NOD, CD45-, PROX [4_6|010|CD45-]

city: Rouen

first: Catalina

last: Abad

address: 22 Blvd Gambetta

country: France

institute: Inserm U1234

data_processing:
FASTQ files were converted into digital count conversion (DCC) and STATS files using GeoMx NGS Pipeline
DCC files were uploaded to the GeoMx DSP to generate the initial, spatially resolved, dataset
Gene counts were mapped to specific ROIs and normalized using Q3 normalization strategy in keeping with NanoString GeoMx recommendations. (https://nanostring.com/resources/introduction-to-geomx-normalization-cta-whitepaper/)
dcc-metadata = false
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: Other: See Mm_R_NGS_WTA_v1.0.pkc Supplementary file
Supplementary files format and content: DCC
Library strategy: Spatial Transcriptomics

source_name: Muscle (quadriceps)

extract_protocol:
Tissues were frozen in chilled in liquid nitrogen for ~ 1,5 min. Six-micrometer-thick cryosections were prepared using the GeoMx Digital Spatial Profiler (DSP) Whole Transcriptome Atlas (WTA) slide prep protocol from NanoString Technologies. Sections were incubated with(WTA RNA-ISH probes conjugated with UV-photocleavable linkers following standard ISH protocols. Entire slides containing Icos+/+ NOD and Icos-/- NOD sections were imaged at ×20 magnification, and Regions of Interest (ROIs) (4 Icos+/+ NOD and 14 Icos-/- NOD) were selected. The GeoMx DSP segmentation tool allowed the separation of different areas of illumination (AOI) on the basis of morphology markers (CD45 and desmin). This strategy allowed the analysis of RNA expression from myofibers (CD45-desmin+) from Icos+/+ NOD (n=4) and from Icos-/- NOD mice, the latter being non-adjacent (designated as “Icos-/- NOD mice PROX”) (n=6) or adjacent (designated as “Icos-/- NOD mice ADJ”) (n=8) to immune cell infiltrate clusters (CD45+desmin-). Regions of interest within the tissue were exposed to UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. DSP protocol detailed information can be found in Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x).
Each collection of oligo tags from one well (corresponding to an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified by AMPure XP PCR purification. Pooled libraries were sequenced at 2 × 27 base pairs and with the dual-indexing workflow on an Illumina NovaSeq 6000.

treatment_protocol: Animals were reared on a 12-hour light-dark cycle and had ad-libitum access to food and water.

value: Muscle (quadriceps)

tag: strain

value: Icos-/- NOD

tag: slide id

tag: roi number

tag: segment type

tag: area

tag: roi x coordinate

tag: roi y coordinate

tag: characteristic


title: Muscle, Icos-/- NOD, CD45+, INF [4_6|009|CD45+]

tag: tissue


title: CD11c+ splenocytes derived from CD300ciCre-hCD2 R26tdTomato mice_RNA

description:
polyA RNA
CD300c_barcodes.tsv.gz
CD300c_features.tsv.gz
CD300c_matrix.mtx.gz

tag: cell type

tag: treatment


title: Muscle, Icos-/- NOD, CD45-, PROX [4_6|008|CD45-]


title: Kidney_WBC_2

value: Kidney

tag: genotype

value: Pcmt1 fl/fl

value: Sham+DMSO


title: Muscle, Icos-/- NOD, CD45-, PROX [4_6|009|CD45-]


title: 1698_Nrf2_KO2

value: Liver

value: Nrf2 KO


title: Muscle, Icos-/- NOD, CD45+, INF [4_6|008|CD45+]


title: Muscle, Icos+/+ NOD, CD45-, WT control [4_6|005|CD45-]

value: Icos+/+ NOD


title: Muscle, Icos+/+ NOD, CD45-, WT control [4_6|006|CD45-]


title: 1670_Gclc_KO1

value: Gclc KO


title: Muscle, Icos-/- NOD, CD45-, ADJ [4_6|002|CD45-]


title: Muscle, Icos-/- NOD, CD45+, INF [4_6|002|CD45+]


title: Muscle, Icos-/- NOD, CD45-, PROX [4_6|004|CD45-]


title: Muscle, Icos-/- NOD, CD45+, INF [4_6|001|CD45+]


title: Muscle, Icos-/- NOD, CD45-, PROX [4_6|003|CD45-]


title: Muscle, Icos+/+ NOD, CD45-, WT control [1_3|009|CD45-]


title: Muscle, Icos-/- NOD, CD45-, ADJ [1_3|007|CD45-]


title: Muscle, Icos-/- NOD, CD45+, INF [1_3|007|CD45+]


title: Muscle, Icos-/- NOD, CD45+, INF [1_3|005|CD45+]


title: Muscle, Icos-/- NOD, CD45-, ADJ [1_3|005|CD45-]


title: Muscle, Icos-/- NOD, CD45-, ADJ [1_3|003|CD45-]


title: Muscle, Icos-/- NOD, CD45-, PROX [1_3|004|CD45-]


title: Muscle, Icos-/- NOD, CD45-, PROX [1_3|002|CD45-]


title: Muscle, Icos+/+ NOD, CD45-, WT control [1_3|008|CD45-]


title: Muscle, Icos-/- NOD, CD45+, INF [1_3|003|CD45+]


title: CKI CDH5 mouse 24

city: Worcester

first: Kate

last: Fitzgerald

state: MA

address: 364 Plantation street, LRB 260E

institute: UMASS Chan Medical School

data_processing:
For Quality Control, we use FastQC to create qc outputs. There are optional read quality filtering (trimmomatic), read quality trimming (trimmomatic), adapter removal (cutadapt) processes available.
RSEM is used to align RNA-Seq reads to a reference transcripts and estimates gene and isoform expression levels. Alternatively, Kallisto used for quantifying abundances of transcripts based on pseudoalignments.
HISAT2, STAR and Tophat2 are used to align RNA-Seq reads to a genome. Optionally, counting reads to genomic features such as genes, exons, promoters and genomic bins could be done by featureCounts.
Assembly: mm10
Supplementary files format and content: A tsv file output by RSEM containing expected counts for detected genes

source_name: Lung

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Micro Kit
Library was prepared using the Illumina mRNA stranded library prep kit

value: Lung

value: Ter119- CD45- stromal cells

value: STING CKI WT x Cdh5-cre ERT2


title: Muscle, Icos-/- NOD, CD45-, ADJ [1_3|001|CD45-]


title: CKI CDH5 mouse 25


title: CKI CDH5 mouse 22


title: CKI CDH5 mouse 23


title: CKI CDH5 mouse 21


title: Muscle, Icos-/- NOD, CD45+, INF [1_3|001|CD45+]


title: CKI CAGG mouse 19

value: STING CKI WT x CAGG-cre ERTM


title: CKI CAGG mouse 20


title: CKI CAGG mouse 16


title: CKI WT mouse 15

value: STING Conditional knock-in (CKI) WT


title: CKI CAGG mouse 17


title: CKI WT mouse 14


title: Muscle, Icos-/- NOD, CD45-, PROX [1_3|006|CD45-]


title: CKI WT mouse 12


title: CKI WT mouse 13


title: Muscle, Icos-/- NOD, CD45-, ADJ [4_6|001|CD45-]


title: VM mouse 10

value: STING V154M mutant


title: VM mouse 8


title: VM mouse 6


title: WT mouse 3

value: WT STING


title: CKI WT mouse 11


title: WT mouse 5


title: WT mouse 4


title: VM mouse 9


title: WT mouse 2


title: VM mouse 7


title: CKI CAGG mouse 18


title: BM ESLAM HSCs, DMSO, Mouse1

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

institute: Shanghai Jiao Tong University School of Medicine

description: 10x Genomics

data_processing:
The sequenced reads were processed with the cellranger pipeline (version 3.1.0) and aligned to the custom reference 10X genomics build mouse mm10 (version 3.0.0) .
Assembly: mm10
Supplementary files format and content: The processed data files were filtered h5 files generated from the standard cellranger pipeline.

extract_protocol:
6K ESLAM HSCs were sorted as CD45+EPCR+CD150+CD48- and cultured in the medium that contains SCF, IL3 and IL-6 to promote STAT5 phosphorylation with or without ruxolitinib for 5 days
The cells were processed with a Chromium Controller according to the Chromium NextGEM Single Cell 3’ GeneExpression v3.1 protocol. The libraries were pooled and sequenced on a Novaseq 6000

value: Bone Marrow

value: ESLAM HSCs

value: WT

value: Cultured in the medium that contains SCF, IL-3 and IL-6 to promote STAT5 phosphorylation without ruxolitinib


title: BM ESLAM HSCs, Rux 250nM, Mouse2

description: 10x Genomics

value: Cultured in the medium that contains SCF, IL-3 and IL-6 to promote STAT5 phosphorylation with ruxolitinib


title: WT mouse 1


title: Liver_Comb._IF (5:2)_5

city: Heidelberg

first: Mathias

last: Heikenwälder

address: Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ) and University of Tuebingen

data_processing:
Nextflow (22.04.0) nf-core/rnaseq pipeline (3.8.1)
Reads were aligned to GRCm38 genome using STAR (nf-core/rnaseq)
Read quantification was done using the RSEM method (nf-core/rnaseq)
Assembly: GRCm38.99
Supplementary files format and content: tab-delimited text file that includes raw, TPM and FPKM counts for each Sample
Supplementary files format and content: tab-delimited text file that includes raw counts for all Samples

extract_protocol:
Livers were flash frozen and RNA was then extracted by Trizol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ppara and Pck1 knockdown

value: Western diet - IF (5:2)


title: BM ESLAM HSCs, Rux 250nM, Mouse1

description: 10x Genomics


title: Liver_Comb._IF (5:2)_3

value: Liver


title: BM ESLAM HSCs, DMSO, Mouse2

description: 10x Genomics


title: Liver_Comb._IF (5:2)_2


title: Liver_Pck1_knockdown_IF (5:2)_5

value: Pck1 knockdown


title: Liver_Pck1_knockdown_IF (5:2)_2


title: Liver_Ppara_knockdown_IF (5:2)_5

value: Ppara knockdown


title: Liver_Pck1_knockdown_IF (5:2)_6


title: Liver_Comb._IF (5:2)_1


title: Liver_Ppara_knockdown_IF (5:2)_2


title: Liver_Pck1_knockdown_IF (5:2)_3


title: Liver_Ppara_knockdown_IF (5:2)_4


title: Liver_Pck1_knockdown_IF (5:2)_1


title: Liver_Scr._IF (5:2)_4

value: Scramble


title: Liver_Scr._IF (5:2)_5


title: Liver_Scr._IF (5:2)_3


title: Liver_Ppara_knockdown_IF (5:2)_1


title: Liver_Comb._A/L_2

value: Western diet - Ad libitum (A/L)


title: Liver_Scr._IF (5:2)_2


title: Liver_Scr._IF (5:2)_1


title: Liver_Comb._IF (5:2)_4


title: Liver_Comb._A/L_4


title: Liver_Comb._A/L_1


title: Liver_Pcl1_knockdown_A/L_4


title: Liver_Pcl1_knockdown_A/L_3


title: Liver_Pcl1_knockdown_A/L_2


title: Liver_Pcl1_knockdown_A/L_1


title: Liver_Ppara_knockdown_A/L_3


title: Liver_Ppara_knockdown_IF (5:2)_3


title: Liver_Ppara_knockdown_A/L_2


title: Liver_Scr._A/L_5


title: Liver_Scr._A/L_4


title: Liver_Scr._A/L_3


title: Liver_Scr._A/L_2


title: Liver_Comb._A/L_3


title: Liver_Scr._A/L_1


title: Liver_Pcl1_knockdown_A/L_5


title: 2-months SAMP8,HTO

city: Zwijnaarde

first: VIB

last: Single Cell Core

address: Technologiepark-Zwijnaarde 71

department: VIB Single cell core

country: Belgium

institute: VIB

description: 10x Genomics

data_processing:
Count matrices were generated using the Cellranger 6.0.0 pipeline (10X genomics)
Raw count matrices were analyzed in seurat 4.0.5, removing cells with less than 3 genes and genes present in less than 200 cells. Replicates were extracted using HTODemux and doublets were excluded. Cells were filtered based on number of UMIs lower than the mean + 2sd, on number of genes between mean +/- 2sd and % mitochondrial genes lower than mean + 2sd
The data was integrated in seurat 4.1.2 using Seurat’s Integrate data regressing out number of UMIs, genes and percentage mitochondrial genes with ScaleData.
Non-microglial cells were excluded from the final objects, these include peripheral macrophage (Mrc1, Cd163), Neutrophils (Retnlg, Mrsb1), Macrophages (Plac8, Adgre5), Proliferating cells (Top2a, Mki67), Choroid plexus cells (Ttr), Endothelial cells (Cldn5, Ly6c1) and doublets/low quality cells (Atp1a2, S100a9) and other immune cells (Gzma, Nkg7). UMAP space and neighbourhood embeddings were calculated based on 18 PC’s. Finally, clustering was performed at a resolution of 0.4 resulting in 6 distinct microglia subpopulations mice for SAMR1 and SAMP8 mice and at a resolution of 0.6 resulting in 5 distinct microglia subpopulations for injected P301L and FVB mice.
Assembly: mm10
Supplementary files format and content: .h5 (count matrices)
Supplementary files format and content: .rds (Seurat object)

source_name: cerebellum and olfactory bulb-removed brains

extract_protocol:
After conducting PBS perfusion and removing the cerebellum and olfactory bulbs, one hemisphere from each mouse were subjected to mechanical and enzymatic dissociation using the GentleMACS™ dissociator (130-093-235, Miltenyi Biotec) in combination with the Neural Tissue Dissociation Kit (130-092-628, Miltenyi Biotec), according to the manufacturer’s instructions. To avoid microglial activation during extraction, we dissociated the hemispheres in the presence of Actinomycin D (5 nM, Sigma-Aldrich SBR00013) and Brefeldin A (1x, 420601 BioLegend). After enzymatic dissociation, cells were resuspended in 30% Percoll (P1644, Sigma-Aldrich) and centrifuged for 15 min at 300 g at 4°C for myelin removal. The supernatant containing the myelin was removed, and the pelleted cells were washed with FACS buffer (PBS, 0.5 % BSA, 2 mM EDTA). Up to 2 million cells per mouse were incubated for 30 min on ice with 25µL of staining mix in PBS containing 0.04% BSA, Cluster of Differentiation CD11b-PE-Cyanine5 antibody (BioLegend, cat 101210), TruStain FcX Block (BioLegend, cat 101320) and a mouse CITE-Seq antibody panel.  The DAPI-CD11b+ cells were subsequently isolated using fluorescence-activated cell sorting (FACS) Aria II.
After FACS sorting cells were spun down, the cell pellet was resuspended and incubated on ice in staining mix and the antibody panel. Replicates were pooled using hahsing antibodies. The cell suspensions were loaded on a Chromium GemCode Single Cell Instrument (10X Genomics) for GEM creation with the 3’ Gel Bead and Library kit version NextGEM 3.1. according to manufacurers instructions.

value: CD11b positive cells

tag: strains

tag: time

tag: Sex

value: Female

value: HTO

value: Hashtag 1 through 8


title: Liver_Ppara_knockdown_A/L_5


title: 2-months SAMR1,HTO

description: 10x Genomics

value: cerebellum and olfactory bulb-removed brains

tag: library type


title: 2-months SAMP8, GEX

description: 10x Genomics

value: mRNA


title: 2-months SAMR1, ADT

description: 10x Genomics

value: ADT

tag: adt

value: list of 158 antibodies


title: 5-months SAMP8, GEX

description: 10x Genomics


title: 5-months SAMR1, GEX

description: 10x Genomics


title: 5-months SAMP8, ADT

description: 10x Genomics

value: list of 174 antibodies


title: 5-months SAMR1,HTO

description: 10x Genomics

tag: hto


title: 5-months SAMR1, ADT

description: 10x Genomics


title: Liver_Ppara_knockdown_A/L_4


title: Liver_Ppara_knockdown_A/L_1


title: 9-months SAMP8, ADT

description: 10x Genomics


title: 9-months SAMR1,HTO

description: 10x Genomics


title: 3-months PI K18-seeded P301L,HTO

description: 10x Genomics

extract_protocol:
After conducting PBS perfusion and removing the cerebellum and olfactory bulbs, contralateral hemispheres (i.e., opposite to the injected hemisphere) were subjected to mechanical and enzymatic dissociation using the GentleMACS™ dissociator (130-093-235, Miltenyi Biotec) in combination with the Neural Tissue Dissociation Kit (130-092-628, Miltenyi Biotec), according to the manufacturer’s instructions. To avoid microglial activation during extraction, we dissociated the hemispheres in the presence of Actinomycin D (5 nM, Sigma-Aldrich SBR00013) and Brefeldin A (1x, 420601 BioLegend). After enzymatic dissociation, cells were resuspended in 30% Percoll (P1644, Sigma-Aldrich) and centrifuged for 15 min at 300 g at 4°C for myelin removal. The supernatant containing the myelin was removed, and the pelleted cells were washed with FACS buffer (PBS, 0.5 % BSA, 2 mM EDTA). Up to 2 million cells per mouse were incubated for 30 min on ice with 25µL of staining mix in PBS containing 0.04% BSA, Cluster of Differentiation CD11b-PE-Cyanine5 antibody (BioLegend, cat 101210), TruStain FcX Block (BioLegend, cat 101320) and a mouse CITE-Seq antibody panel.  The DAPI-CD11b+ cells were subsequently isolated using fluorescence-activated cell sorting (FACS) Aria II.
After FACS sorting cells were spun down, the cell pellet was resuspended and incubated on ice in staining mix and the antibody panel. Replicates were pooled using hahsing antibodies. The cell suspensions were loaded on a Chromium GemCode Single Cell Instrument (10X Genomics) for GEM creation with the 3’ Gel Bead and Library kit version NextGEM 3.1. according to manufacurers instructions.

treatment_protocol: At the age of 90 ± 5 days, FVB and P301L mice were deeply anaesthetised with isoflurane (2% in 36% oxygen) and fixed in a stereotactic frame (Neurostar, Germany, Stereodrive software v 2019). A 30G syringe (Hamilton) was used for injecting 2 μl of PBS or K18 (7.5 µg) in the right hemisphere at a speed of 0.2 μl/min at the selected coordinates: anterior-posterior −2.0 mm, medial-lateral +1.6 mm from Bregma, and dorsal-ventral +1.4 mm from the dura.

tag: strain

tag: timepoint

value: 3-months PI

value: male

value: Hashtag 1 through 12


title: 9-months SAMR1, ADT

description: 10x Genomics


title: 9-months SAMP8, GEX

description: 10x Genomics


title: 5-months SAMP8,HTO

description: 10x Genomics


title: 3-months PI K18-seeded P301L, GEX

description: 10x Genomics


title: 3-months PI K18-seeded P301L, ADT

description: 10x Genomics


title: 3-months PI PBS-injected P301L,HTO

description: 10x Genomics

value: PBS-injected


title: 9-months SAMR1, GEX

description: 10x Genomics


title: 3-months PI PBS-injected P301L, ADT

description: 10x Genomics


title: 2-months SAMP8, ADT

description: 10x Genomics


title: 3-months PI PBS-injected FVB,HTO

description: 10x Genomics

value: FVB/NJ


title: 3-months PI PBS-injected FVB, ADT

description: 10x Genomics


title: 3-months PI PBS-injected FVB, GEX

description: 10x Genomics


title: flox-the tastrocnemius muscle of TECRLflox/flox mice

city: Suzhou

first: Wei

last: He

state: Jiangsu

address: 199 RenAi Road

department: Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology

institute: Soochow University

data_processing:
Illumina Casava  bcl2fastqv2.19 software used for basecalling.
Filter the Raw Reads obtained by sequencing to obtain clean Reads that can be used for data analysis, and apply Seqtk to filter. The main steps are as follows: 1. Remove the linker sequence contained in the reads; 2. Remove the 3'end quality Q less than 20 Bases, that is, the base error rate is less than 0.01, where Q=-10logerror_ratio; 3. Removal of reads less than 25 in length; 4. Removal of ribosome RNA reads of the species.
Use Hisat2 (version: 2.0.4) split mapping algorithm to perform Genome mapping on the preprocessed reads. This algorithm allows the splitting of reads that cannot be matched to the full length to be mapped, and is more suitable for eukaryotic (with intron inter-regions). ) Transcriptome sequencing data; default parameters are used.
In transcriptome sequencing, we can estimate the level of gene expression by mapping the number of reads to the gene region, but the number of reads is not only proportional to the level of gene expression, but also related to the length of the gene itself and the amount of sequencing data. In order to make the gene expression levels of different genes and different samples comparable, the reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) to standardize the gene expression levels.
We first use Stringtie (version: 1.3.0) to count the number of Fragments of each gene after Hisat2 comparison, then use the TMM (trimmed mean of M values) method to normalize, and finally use the perl script to calculate each gene FPKM value.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: muscle

extract_protocol:
Total RNA was extracted using the RNAsimple total RNA Kit (Cat# DP419, Tiangen) according to manufacturer’s instructions.
The library construction is based on illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ).
Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina novaseq6000. The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).

value: muscle

value: TECRLflox/flox


title: 1-month PI K18-seeded P301L,HTO

description: 10x Genomics

value: 1-month PI


title: 1-month PI K18-seeded P301L, ADT

description: 10x Genomics

value: CD11b positive cells


title: 1-month PI K18-seeded P301L, GEX

description: 10x Genomics


title: 3-months PI PBS-injected P301L, GEX

description: 10x Genomics


title: 1-month PI PBS-injected P301L, ADT

description: 10x Genomics


title: 1-month PI PBS-injected FVB,HTO

description: 10x Genomics


title: 2-months SAMR1, GEX

description: 10x Genomics

value: Female


title: 1-month PI PBS-injected FVB, ADT

description: 10x Genomics


title: 1-month PI PBS-injected P301L, GEX

description: 10x Genomics


title: 1-week PI K18-seeded P301L,HTO

description: 10x Genomics

value: 1-week PI

value: HTO


title: 1-week PI K18-seeded P301L, GEX

description: 10x Genomics

value: cerebellum and olfactory bulb-removed brains


title: 1-week PI PBS-injected P301L,HTO

description: 10x Genomics


title: 1-week PI K18-seeded P301L, ADT

description: 10x Genomics


title: 1-week PI PBS-injected P301L, ADT

description: 10x Genomics


title: 1-month PI PBS-injected FVB, GEX

description: 10x Genomics

value: mRNA


title: 1-week PI PBS-injected P301L, GEX

description: 10x Genomics


title: 1-week PI PBS-injected FVB,HTO

description: 10x Genomics


title: 1-week PI PBS-injected FVB, ADT

description: 10x Genomics

value: ADT


title: 1-month PI PBS-injected P301L,HTO

description: 10x Genomics


title: 1-week PI PBS-injected FVB, GEX

description: 10x Genomics


title: Ta3-3

city: Beijing

first: Yunshu

last: Wu

address: No.22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: xenograft

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: xenograft

tag: cell line

value: primary cells

value: macrophages

value: WT

value: cultured on Zr58Cu25Al14Ta3 MG


title: Ta3-2


title: Ta3-1


title: Ta0-1

value: cultured on Zr61Cu25Al14 MG


title: cpTi1

value: cultured on cpTi


title: scko-the tastrocnemius muscle of TECRLscko mice

value: muscle

value: TECRLscko


title: Ctrl replicate2 scRNA-seq

city: Guangzhou

first: Yunxing

last: Shi

address: Erheng Road, Member Village, Tianhe District

institute: sun-yat sen university

description: 10X Genomics

data_processing:
The CellRanger (6.1.2) pipeline was used for demultiplexing, barcode processing, alignment, and initial clustering of the raw scRNA-seq profiles. Raw sequencing reads were then aligned to the human genome (GRCh38, ENSEMBL). We then used Seurat (V4.3.0) to process the unique molecular identifier (UMI) count matrix and integrate all cells according to sample ID by using Harmony
Assembly: mm10
Supplementary files format and content: molecular info files and matrixs files

source_name: Tumor cells

extract_protocol:
Tumor tissue was incubated in dissociation buffer containing 2 mg/ml Collagenase Ⅳ(sigma,C5138), 2 mg/ml Collagenase II sigma C6885， 10 mg/ml Dispase II (corning,354235) and 50,000U/ml DNase I (sigma, DN25) for 30 min at 37 °C. Enzymatic digestion was quenched with Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal calf serum (FCS, 10270106, Gibco). Cells were resuspended at a concentration of 1 million cells per ml and stained with PBST containing 1% FCS. Then 15 µl of single-cell suspension at a concentration of ~900,000 cells/ml was loaded into one channel of the ChromiumTM Single Cell B Chip (10X Genomics，1000073), aiming for a recovery of 8000–9000 cells.
The Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10X Genomics, 1000075) was used for single-cell barcoding, cDNA synthesis and library preparation, following the manufacturer’s instructions according to the Single Cell 3′ Reagent Kits User Guide Version 3.

value: Tumor cells

value: HCC cell line


title: Ctrl replicate3 scRNA-seq

description: 10X Genomics


title: cpTi2


title: Ctrl replicate1 scRNA-seq

description: 10X Genomics


title: Prmt3 KO replicate2 scRNA-seq

description: 10X Genomics

value: Prmt3 KO


title: Prmt3 KO replicate3 scRNA-seq

description: 10X Genomics


title: ATAC_BPA_rep4

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

data_processing:
Raw data were first analyzed by FastQC for quality control and then filtered out adaptor and low-quality reads by Trim-galore (--quality 20 --phred33 --stringency 1 --length 20) to obtain clean data.
Clean data were mapped to the reference genome (UCSC, mm10) using Bowtie2 v2.4.1 with parameters set as: -X 1000.
SAMtools v1.6 were used to convert SAM files to BAM files, sort and build the alignment file index.
Bigwig files were generated using bamCoverage with parameters set as: --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX chrM
Assembly: mm10
Supplementary files format and content: Tab-delimited bigwig text files for each sample

source_name: neuron

extract_protocol:
Cortex were homogenized in the lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM MgAce2, 0.1 mM EDTA, 10 mM Tris-HCl, pH = 8, 0.1% NP-40), and neuronal (NeuN+) nuclei were enriched by FACS sorting using MoFlo Astrios EQ cell sorter (Beckman Counter).
Chramotin were digested with 5 μl of Tn5 enzyme in 50 μl of digestion buffer (TD501-02, TruePrep DNA Library Preparation Kit V2, Vazyme, China) at 37 ◦C for 30 min. MinElute gel extraction kit (Qiagen, 28604) was used for DNA purification. Then, DNA was eluted in 24 μl of EB buffer and subjected to the PCR amplification with the reaction set as follows:24 μl of DNA,5 μl of PPM, 10 μl of 5 × TAB, 5 μl of N7 primer, 5 μl of N5 primer, and 1 μl of TAE buffer, and the PCR programming was: 72 ◦C for 3 min,98 ◦C for 30 s, 11 cycles of amplification: 98 ◦C for 30 s, 60 ◦C for 30 s, 72 ◦C for 30 s. Library DNA was purified using SPRI magnetic beads (Beckman, B23318) with a size between 150 bp and 500 bp was selected. The quality of the library was evaluated by Agilent 4200 TapeStation, and the concentration was measured with Qubit4. The library was then sent for sequencing on Novaseq6000 set paired-end, 150 bp (PE150).

treatment_protocol: Timed-pregnant C57BL/6Slac mice were randomly assigned into two groups, receiving either corn oil (Ctrl) or BPA (40 ug/kg bw/day) administered by oral gavage from gestational day 0.5 to 13.5.

value: cortex

tag: age

value: 4 months

value: male

value: BPA (40 ug/kg bw/day)

tag: mouse id


title: ATAC_BPA_rep5


title: Prmt3 KO replicate1 scRNA-seq

description: 10X Genomics


title: PD-1-KO-UUO3-K

first: Yi

last: Zhou

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-Sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  MT% < 20%;   Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: Single cell matrix files

source_name: kidney

extract_protocol:
Pulmonary artery tissues were placed in DMEM/F12(Gibco), and cut into small fragments and digested them with collagenase II (Invitrogen) for 2h at 37℃. After digestion, the obtained cells were filtered through a 70μm filter and collect it into a collection tube.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

treatment_protocol: Groups of male mice were anesthetized by intraperitoneal injection of 0.5% sodium pentobarbital, and the left ureter was ligated twice with silk sutures before being cut. The mice were kept at a constant body temperature of 37 °C. Sham-operated mice had their ureters exposed and manipulated without ligation.

value: kidney

value: Innate lymphoid cells

value: 8-10 weeks old

value: 3 days post UUO surgery


title: 9-months SAMP8,HTO

description: 10x Genomics

value: cerebellum and olfactory bulb-removed brains

value: CD11b positive cells

value: Female

value: HTO

value: Hashtag 1 through 8


title: WT-UUO3-K

value: wild type

value: 3 days post unilateral ureteral obstruction (UUO) surgery


title: Ta0-2

value: xenograft

value: primary cells

value: macrophages

value: WT

value: cultured on Zr61Cu25Al14 MG


title: WT-UUO3-SI

source_name: small intestine

value: small intestine

value: Group 3 innate lymphoid cells


title: ATAC_Ctrl_rep3

value: cortex

value: 4 months

value: male

value: Corn oil


title: ATAC_Ctrl_rep4


title: ATAC_Ctrl_rep2


title: cpTi3

value: cultured on cpTi


title: ATAC_Ctrl_rep5


title: H3K9me3_BPA_rep4

data_processing:
Raw data were first analyzed by FastQC for quality control and then filtered out adaptor and low-quality reads by Trim-galore (--quality 20 --phred33 --stringency 1 --length 20) to obtain clean data.
clean data were mapped to the reference genome (UCSC, mm10) using Bowtie2 v2.4.1 with default settings.
SAMtools v1.6 were used to convert SAM files to BAM files, sort and build the alignment file index.
Bigwig files were generated using bamCoverage with parameters set as: --binSize 10 --normalizeUsing RPKM --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX chrM
Assembly: mm10
Supplementary files format and content: Tab-delimited bigwig text files for each sample

source_name: cortex

extract_protocol:
Cortex homogenate was used for H3K27me3 ChIP. As for H3K9me3, Nuclei was extracted from the cortex of male offspring and neuronal (NeuN+) nuclei were enriched by FACS sorting using MoFlo Astrios EQ cell sorter (Beckman Counter). nuclei were suspended in the MNase digestion buffer (10 mm Tris, pH 7.5, 4 mm MgCl2, and 1 mM Ca2+) and chromatin was digested with MNase at 28 ℃ for 10 min to obtain mononucleosomes and incubated with H3K9me3 (Abcam AB8898) and H3K27me3 (Millipore, 07-449) antibody at 4 ℃ overnight. The immunoprecipitated complexes were captured by Protein AG Magnetic Beads (Thermo Scientific 88803) and washed with 1 mL low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris, 150 mM NaCl), 1 mL high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris, 500 mM NaCl), 500 uL Lithium Cloride buffer (1% IGEPAL-CA 630, 1% Deoxycholic acid, 1 mM EDTA, 10 mM Tris, 0.25 M LiCl), 1 mL TE buffer (1 mM EDTA, 10 mM Tris). ChIP DNA was eluted in 60 uL Elution buffer (0.1M NaHCO3, 1% SDS) and incubated with RNase A, followed by proteinase K incubation. Finally, ChIP DNA was purified using SPRI magnetic beads (Beckman, B23318).
End-repairing (Lucigen Corporation, ER0720) and A-tailing (Lucigen Corporation, KL11101K) was performed and then ChIP DNA was ligated (Lucigen Corporation, LK0750H) with Y-adaptor (Vazyme, N802) and subjected to PCR amplification (Vazyme, N618-01).

value: BPA (40 ug/kg bw/day)


title: ATAC_BPA_rep1


title: ATAC_Ctrl_rep1


title: H3K9me3_BPA_rep5


title: H3K9me3_Ctrl_rep4


title: H3K9me3_BPA_rep3


title: H3K9me3_Ctrl_rep3


title: WT-sham-SI

value: 8-10 weeks old

value: sham surgery


title: H3K9me3_Ctrl_rep2


title: ATAC_BPA_rep3


title: WT-UUO14-K

value: kidney

value: wild type

value: Innate lymphoid cells

value: 14 days post UUO surgery


title: H3K27me3_BPA_rep4

value: BPA (41 ug/kg bw/day)


title: H3K9me3_Ctrl_rep1


title: H3K27me3_BPA_rep2


title: H3K27me3_BPA_rep3


title: H3K27me3_Ctrl_rep4


title: H3K27me3_Ctrl_rep2


title: H3K27me3_BPA_rep1


title: RRBS_BPA_rep3

description: MspI

data_processing:
Sequenced reads were filtered and trimmed with “fastp” () (version 0.23.4, -q 20 -u 50 -n 5)
Clean data were aligned to the mouse genome mm10 and lambda phage genome with Bowtie2 () (version 2.2.3) in default settings
Aligned reads were deduplicated with “deduplicate_bismark” function of Bismark (version 0.22.1).
The “bismark_methylation_extractor” function of Bismark (--no_overlap --ignore_r2 2 --comprehensive) were used to extract methylation information, and the bisulfite conversion rate was calculated according to the methylation level of spiked-in lambda DNA
Assembly: mm10
Supplementary files format and content: Tab-delimited coverage text files for each sample

extract_protocol:
Nuclei was extracted from cortex homogenates and incubated with 5 ul of 10 mg/mL RNaseA (Sigma R6513) in 500 ul PK lysis buffer (1 M Tris pH8, 50 mM EDTA, 2% SDS, 2 M NaCl) at 37 ℃ for 15 minutes, followed by 10 μl of 20 mg/mL proteinase K (Sigma P2308) incubation at 52 ℃ overnight. The samples were then added with phenol/chloroform (1:1) (Solarbio P1021), mixed with vortex, and centrifugated with 15000 g at RT for 10 minutes. The supernatant was taken and precipitated with isopropanol. The precipitated genomic DNA (gDNA) was washed in 70% ethanol, air dried and dissolved in buffer EB (Qiagen 19086). A total of 1 ug DNA was used for for RRBS library preparation.
gDNA was spiked in with unmethylated lambda DNA and incubated with MspI enzyme to obtain 200 to 1000 bp fragments. The DNA fragments were then subjected to bisulfite conversion for converting any unmethylated cytosine to Uracil by EZ DNA Methylation-Gold Kit (Zymo Research, United States). The Accel-NGS® Methyl-Seq DNA Library Kit (Swift, MI) was used for library preparation and 200-400 bp DNA fragments were purified for further sequencing.


title: H3K27me3_Ctrl_rep3


title: RRBS_BPA_rep2

description: MspI


title: RRBS_Ctrl_rep3

description: MspI


title: RRBS_Ctrl_rep2

description: MspI


title: RRBS_Ctrl_rep1

description: MspI


title: H3K9me3_BPA_rep2


title: KO_HR_IgG_cut&run

city: Ann Arbor

first: Wenbin

last: Gao

state: MI

address: NCRC 2800 Plymouth

institute: University of Michigan

data_processing:
For RNA-seq, the transcript abundance is quatifiy using Kallisto.
For Cut&Run seq, the reads were trimmed using Trimmomatic, and then aligned to mouse genome using bowite2 with --dovetail option. The bam files were then converted into bedgraph format. The peaks were called using SECAR.
Assembly: mm10
Supplementary files format and content: tsv files are RNA quantification files using kallisto
Supplementary files format and content: cut&run peaks are called H3k27ac/K9ac/Acly vs IgG using SECAR. Files are in bed format.
Library strategy: CUT&Run

source_name: Primary hepatocytes

extract_protocol:
The cut&run assay was performed using CST cut&run kit following the manufacturer's protocol. RNA was extracted from liver tissue using trizol-qiagen hybrid protocol with on-column DNA digestion.
The library was prepared using NEB ultraII DNA library kit.

value: Primary hepatocytes

tag: antibody

value: Normal Rabbit IgG, CST#2729

value: AclyKO

value: Hypoxia-reperfusion


title: H3K9me3_BPA_rep1

value: cortex


title: Ta0-3

value: xenograft

value: primary cells

value: macrophages

value: WT

value: cultured on Zr61Cu25Al14 MG


title: KO_HR_H3K27ac_cut&run

value: Millipore A-ACET-HIST H3(K27) 100UL 07-360


title: WT_HR_Acly_cut&run

value: sigma Monoclonal ANTI-FLAG® M2 antibody produced in mouse F3165-.2MG mouse


title: WT_HR_H3K9ac_cut&run

value: Millipore A-ACETYL-HIST H3 (LYS9) 100UL 07-352


title: WT_HR_H3K27ac_cut&run


title: WT_normoxia_IgG_cut&run

value: Normoxia


title: WT_normoxia_Acly_cut&run


title: KO_HR_H3K9ac_cut&run


title: RRBS_BPA_rep1

description: MspI

value: 4 months

value: male

value: BPA (40 ug/kg bw/day)


title: H3K27me3_Ctrl_rep1

value: Corn oil


title: Primary T cells, DC SPI13

city: Hang Zhou

address: Huansha Roud

institute: Zhejiang University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus_musculus_Ensembl_106
Supplementary files format and content: tab-delimited text file includes gene counts for each Sample

source_name: Primary T cells

growth_protocol: Primary T cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Incubated with DC cells treated with DB2313.

value: Primary T cells

value: incubated with DC cells treated with DB2313


title: WT_normoxia_H3K9ac_cut&run

value: Primary hepatocytes


title: WT_normoxia_H3K27ac_cut&run


title: Primary T cells, DC SPI12


title: Primary T cells, DC SPI11


title: Primary T cells, DC2

value: incubated with DC cells


title: Primary T cells, DC1


title: Primary T cells, DC3


title: dendritic cell, DB2313 3

data_processing:
Illumina Casava 1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Mus_musculus_Ensemble_106
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: dendritic cell

growth_protocol: DCs  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Treated with DB2313y or not.

value: dendritic cell


title: dendritic cell, DB2313 2


title: dendritic cell 2

value: Control


title: dendritic cell 3


title: WT_HR_IgG_cut&run

value: Normal Rabbit IgG, CST#2729

value: Hypoxia-reperfusion


title: Tumor infiltrating CD4 T cell，7D4

source_name: Tumor infiltrating CD4 T cell

growth_protocol: Tumor infiltrating CD4 T cells were sorted from tumor of mice hepatocellular carcinoma orthotopic transplantation model.

treatment_protocol: Mice hepatocellular carcinoma orthotopic transplantation model were eatablished for 0 day or 7 day.

value: Tumor infiltrating CD4 T cell

value: 7 Day


title: Tumor infiltrating CD4 T cell，7D5


title: Tumor infiltrating CD4 T cell，7D3


title: Tumor infiltrating CD4 T cell，7D2


title: Tumor infiltrating CD4 T cell，7D1


title: dendritic cell 1


title: Tumor infiltrating CD4 T cell，0D2

value: 0 Day


title: Tumor infiltrating CD4 T cell，0D1


title: 1M_Sham_3

city: Columbia

first: Rong

last: Li

address: 1030 Hitt Str

department: OBGYN

institute: University of Missouri

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
The raw reads were initially filtered by removing low quality reads (average quality scores < 20) and aligned to the mm39 genome and assembled using Star 2.7.9a.
The differentiated expressions of genes (DEGs) were determined by the exact test of EdgeR.
Assembly: mm39
Supplementary files format and content: raw_counts.txt

source_name: Uterus

growth_protocol: Endometriosis or sham surgery were performed in eight weeks old mice.

extract_protocol:
The total RNA was isolated by the RNeasy Total RNA Isolation Kit (Qiagen) following the manufacture’s manual
cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters

treatment_protocol: 1M or 3M after surgery, the mice were mated with stud male. And the eutopic, ectopic or sham endometrium were collected at pregnancy day 3.5.

value: Uterus

tag: disease status

value: sham

tag: endometrial location

value: sham eutopic

tag: collection

value: Pregnancy day 3.5

tag: fertiliuty

value: fertilie

tag: strain background

value: mixed C57BL/6 and SV129


title: 1M_Sham_4

tag: tissue

tag: genotype


title: 3M_Sham_4


title: 3M_Sham_2


title: 3M_Sham_3


title: dendritic cell, DB2313 1

tag: cell type

tag: treatment


title: 3M_Sham_1


title: 1M_Sham_1


title: 1M_Ectopic_4

value: endometriosis

value: Ectopic


title: 1M_Ectopic_3


title: ATAC_BPA_rep2

value: cortex

value: 4 months

tag: Sex

value: male

value: BPA (40 ug/kg bw/day)


title: 3M_Ectopic_3

value: subfertile


title: 3M_Ectopic_2


title: 1M_Ectopic_1


title: 3M_Ectopic_1


title: 3M_Ectopic_4


title: 1M_Eutopic_1

value: Eutopic


title: 3M_Eutopic_3


title: 1M_Eutopic_2


title: 1M_Eutopic_3


title: 3M_Eutopic_2


title: 3M_Eutopic_1


title: 3M_Eutopic_4


title: Jurkat T cells Matr3 KO 2

source_name: Jurkat T cells

growth_protocol: Jurkat T cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Knock out MATR3 by crisp cas9 or not

value: Jurkat T cells

value: T cell

value: Matr3 knock out


title: 1M_Sham_2

value: Uterus


title: Jurkat T cells Matr3 KO 1


title: Jurkat T cells 2

value: wildtype


title: Jurkat T cells 1


title: 1M_Ectopic_2


title: SHAM-GH-1

city: guangzhou

first: guangsen

last: wu

address: 广东省广州市广州大道北1838号南方医科大学南方医院

institute: Southern Medical University Nanfang Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Hypothalamus

growth_protocol: Brain tissue was removed and stored in liquid nitrogen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Hypothalamus

value: Sham+GH

tag: time

value: Day 0


title: SHAM-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院

value: Sham


title: SHAM-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: SHAM-GH-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_10d-GH-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院

value: Pituitary stalk electrical lesion (PEL)+GH

value: Day 10


title: SHAM-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_10d-GH-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: SHAM-GH-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: 1M_Eutopic_4

value: endometriosis

value: Pregnancy day 3.5

value: fertilie

value: mixed C57BL/6 and SV129


title: PEL_10d-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院

value: Pituitary stalk electrical lesion (PEL)


title: PEL_10d-GH-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_3d-GH-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院

value: Day 3


title: PEL_10d-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_3d-GH-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_3d-GH-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_3d-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_3d-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: PEL_3d-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: HIP-SHAM-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: HIP-SHAM-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院

source_name: hippocampus

value: hippocampus


title: PEL_10d-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: HIP-SHAM-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: HIP-PEL_10d-3

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: adipocyte_siGLS_rep3

city: Stockholm

first: Jiawei

last: Zhong

address: Blickagången 16, Flemingsberg

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Raw sequencing files were processed using CASAVA software with default settings, generating Fastq files for further downstream mapping and analysis
Fastq files were aligned to hg38 Human genome using STAR aligner tool
We next quantified reads for each gene transcript to generate a raw counts table
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes counts for each Samples

extract_protocol:
total RNA was extracted from in vitro differentiated human white adipocytes with column based method, as specified in the method section of the manuscript
100ng of total RNA were used to generate a library, cDNA libraries across samples were normalized and combined, the pool was therefore sequenced on Illumina Nextseq 2000 P2, 100 cycles sequencing run

value: siGLS


title: adipocyte_siGLS_rep2

source_name: in vitro differentiated human white adipocytes


title: HIP-PEL_10d-2

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: HIP-PEL_10d-1

address: 广东省广州市广州大道北1838号南方医科大学南方医院


title: adipocyte_siGLS_rep1

value: in vitro differentiated human white adipocytes


title: Stat5-/- aged sample #90

city: Cambridge

first: Hugo

middle: P.

last: Bastos

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: Wellcome - MRC Cambridge Stem Cell Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v2.1.1 ( https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: h5 compressed file with filtered UMI counts

source_name: bone marrow

extract_protocol:
The femora, tibiae, and ilia of C57BL/6 mice of WT and STAT5ab mice were crushed and the bone marrow cells were released and the red blood cells were lysed with ammonium chloride solution (STEMCELL Technologies). The cells were stained with the fluorophore-conjugated monoclonal antibodies, and sorted using an Influx cell sorter (BD Biosciences) equipped with five lasers. The cells were sorted into 1.5 ml tubes containing PBS + 2% FCS. Sorted cells were harvested, resuspended in 0.04% BSA (Thermo Fisher) and counted. Cells were processed using the 10x Chromium™ Single Cell 3' kit (v2), following manufacturers instructions.
Libraries were prepared using 10x Chromium™ Single Cell 3' kit (v2), following manufacturers instructions. Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A mRNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled cell barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction P5, P7, a sample index, and an Ilumina Read 2 are added (via End Repair, A-tailing, Adaptor Ligation, and PCR). The resulting libraries contain the P5 and P7 primer sequences required for Illumina sequencing.

value: bone marrow

value: 12 months

value: Lin-cKit+

value: Stat5 KO

tag: index library


title: adipocyte_siC_rep2

value: siC


title: STAT5ab +/+ Cre+/- (WT) 24366 N336

description: 10x Genomics

value: 3 months

value: WT


title: adipocyte_siC_rep3


title: WT aged sample #89

description: 10x Genomics


title: CD34+ HSPCs SF3B1 mutant

city: Pavia

first: Martina

last: Sarchi

address: Via Ferrata 9

department: Dept. of Molecular Medicine

country: Italy

institute: University of Pavia

data_processing:
Data was aligned to hg38 reference genome using CellRanger.
CellRanger output was read into single cell format count matrices using Scanpy read_10x_mtx function: aavsi_matrix.h5ad and sf3bi_matrix.h5ad
The two count matrices were concatenated to create the Anndata object for subsequent data analysis in Scanpy.
Data filtering involved removing cells with <200 expressed genes, UMI < 5000, mitochondrial reads >=10%, and genes expressed in <3 cells.
Doublets were removed using Scrublet.
Assembly: hg38
Supplementary files format and content: aavsi_matrix.h5ad and sf3bi_matrix.h5ad are h5ad single cell matrices that have not undergone any processing
Supplementary files format and content: filtered_ad.h5ad is a single cell matrix that contains filtered count data for both control (AAVS1) and SF3B1 samples

source_name: Hematopoietic

growth_protocol: HSPCs were cultured in StemSpan SFEM II (StemCell Technologies), 100 U/mL penicillin/streptomycin (Fisher), 100 ng/ml SCF, 100 ng/ml FLT3, 100 ng/ml TPO, 100 ng/ml IL-6 (all Peprotech), 35 nM UM171 (Apexbio Technology) and 0.75 μM SR1 (Cellagen Technology).

extract_protocol:
Single cell sequencing was performed using the 10X Chromium Next GEM Single Cell 3’ Reagents kit v.3.1 on a Chromium Controller.
The library was prepared according to the 10X Genomics manufacturer protocol.

treatment_protocol: CD34+ HSPCs were gene edited for SF3B1 K700E or control (AAVS1), BFP+CD34+ edited cells were isolated by flow sorting after 72 hours and resuspended in 2% BSA.

value: Hematopoietic

value: CD34+ HSPCs


title: A549 RSV-infected, total RNA 2

city: Edinburgh

first: José

middle: Roberto

last: Bermúdez-Barrientos

state: Lothian

address: Charlotte Auerbach Rd

department: Institute of Immunology & Infection

institute: The University of Edinburgh

description: RSV IN 2

data_processing:
adapter trimming and quality filters with trimmomatic PE -phred33 ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
alignment to the genome with hisat2 --non-deterministic in paired-end mode
samtools to convert to bam file, sort and index alignments
counted reads in features with featureCounts implemented in Rsubread 2.12.3 R package, with params: GTFattrType="gene_id", isPairedEnd = TRUE, primaryOnly = FALSE, countMultiMappingReads = TRUE, isGTFAnnotationFile = TRUE, allowMultiOverlap = FALSE, fraction=TRUE, fracOverlap =0, largestOverlap=TRUE, requireBothEndsMapped=FALSE, checkFragLength=FALSE, minOverlap=1, strandSpecific = 2
Assembly: GRCh38.primary_assembly.genome.fa taken from Gencode 34
Supplementary files format and content: csv containing gene_symbol, biotype, chr, gene_id and counts for each gene or regulatory region in the genome

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using miRNeasy kit (Qiagen) with on-column DNase digest (Qiagen)
Libraries were generated using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina and the NEBNext rRNA Depletion kit (Human/Mouse/Rat) according manufacture's instructions.

treatment_protocol: Cells were either Mock or RSV-infected (MOI 0.1) for 48h, then the cells were lysed and 1/10 was used for total RNA, 9/10 were used for AGO2 IP

value: lung epithelial

value: RSV-infection


title: Primary T cells 5 control input

last: Xu

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm39.104 whole genome usingBWA (v 0.7.12)with parameters BWA mem ( v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment,significant level and peak summit number per peak were all displayed.
Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: Mus_musculus_Ensemble_GRCm39.104
Supplementary files format and content: tab-delimited text files  peak  for each Sample

extract_protocol:
RNA was harvested using Trizol reagent.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary T cells were treated with PTC  for 24hours

value: Primary T cells

value: control


title: A549 miR-27a & miR-27b inhibitor transfected, Mock-infected,rep 3

description: 34_27ab Inhibitor Mock

extract_protocol:
Cells were harvested in Qiazol and RNA was extracted using miRNeasy kit (Qiagen) with on-column DNase digest (Qiagen)
Libraries were generated using the NEBNext Ultra 2 Directional RNA library prep kit for Illumina and the NEBNext rRNA Depletion kit (Human/Mouse/Rat) according manufacture's instructions.

treatment_protocol: Cell were seeded or reverse transfected for 24h and subsequently either Mock or RSV-infected (MOI 0.1) for 48h

value: lung epithelial cells

value: miR-27a & miR-27b inhibitor transfected

value: Mock-infection


title: A549 Mock-infected, total RNA 2

description: Mock IN 2


title: A549 RSV-infected, total RNA 3

description: RSV IN 3


title: A549 Mock-infected, total RNA 3

description: Mock IN 3


title: Primary T cells 6 control input


title: A549 Mock-infected, total RNA 1

description: Mock IN 1


title: CD34+ HSPCs AAVS1 control

description: 10X Chromium Next GEM Single Cell 3’ Reagents kit v.3.1


title: Primary T cells 8 PTC input

value: PTC


title: STAT5ab F/- Cre-/- (WT) 24362 N335

description: 10x Genomics

value: bone marrow


title: Primary T cells 3 PTC IP

tag: fraction

value: m6A-binding RNA


title: A549 RSV-infected, total RNA 1

description: RSV IN 1

tag: cell line


title: Primary T cells 7 PTC input


title: STAT5ab F/F Cre+/- (Stat5-/-) 24363 N335

description: 10x Genomics

tag: age

value: Lin-cKit+


title: Primary T cells 2 control IP


title: A549 control inhibitor transfected, Mock-infected,rep 2

description: 32_CTRL Inhibitor Mock

value: control inhibitor transfected


title: Primary T cells 1 control IP


title: A549 miR-27a & miR-27b mimic transfected, Mock-infected,rep 3

description: 33_27ab Mimic Mock

value: miR-27a & miR-27b mimic transfected


title: primary T cells ，PTC 2

source_name: primary T cells

growth_protocol: Primary T cells  were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) ，IL2，CD3/28 beads and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Treated with PTC or not.

value: primary T cells


title: A549 control mimic transfected, Mock-infected,rep 2

description: 31_CTRL Mimic Mock

value: control mimic transfected


title: A549 miR-27a & miR-27b mimic transfected, Mock-infected,rep 2

description: 29_27ab Mimic Mock


title: A549 miR-27a & miR-27b inhibitor transfected, Mock-infected,rep 2

description: 30_27ab Inhibitor Mock


title: primary T cells ，PTC 1


title: primary T cells 2

value: Control


title: adipocyte_siC_rep1

value: in vitro differentiated human white adipocytes

value: siC


title: STAT5ab F/F Cre+/- (Stat5-/-) 24365 N336

description: 10x Genomics

value: 3 months

value: Stat5 KO


title: A549 control inhibitor transfected, Mock-infected,rep 1

description: 28_CTRL Inhibitor Mock


title: primary T cells 1


title: Xenograft tumor-DFMO-scRNA-seq

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

data_processing:
The CellRanger(V3.02)  was used to demultiplex the raw data and scanpy(v1.4.4) was utilized the following procedure to control for data quality: cells with fewer than 200 genes, and genes that are detected in less than 5 cells
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw counts  for each cell

source_name: Xenograft tumor

growth_protocol: in SPF standard environment

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 5% v/v FBS for further library construction
RNA libraries were prepared with Chromium Single cell 5'Library & Gel Bead according to the manufacturer's protocol.

treatment_protocol: gavage with DFMO or water twice a day for 14 days since 7-days after tumor incubation

tag: strain

value: xenograft-derived immune cells

value: DFMO


title: Xenograft tumor-Water-scRNA-seq

value: water


title: KOIRrna_2

data_processing:
For RNA-seq, the transcript abundance is quatifiy using Kallisto.
For Cut&Run seq, the reads were trimmed using Trimmomatic, and then aligned to mouse genome using bowite2 with --dovetail option. The bam files were then converted into bedgraph format. The peaks were called using SECAR.
Assembly: mm10
Supplementary files format and content: tsv files are RNA quantification files using kallisto
Supplementary files format and content: cut&run peaks are called H3k27ac/K9ac/Acly vs IgG using SECAR. Files are in bed format.

source_name: liver

value: liver

value: Hypoxia-reperfusion


title: A549 miR-27a & miR-27b mimic transfected, Mock-infected,rep 1

description: 25_27ab Mimic Mock

value: lung epithelial cells

value: Mock-infection


title: KOIRrna_4


title: A549 WT, Mock-infected rep 2

description: 12_A549 WT Mock

value: WT


title: A549 WT, Mock-infected rep 3

description: 18_A549 WT Mock


title: A549 miR-27a & miR-27b inhibitor transfected, Mock-infected,rep 1

description: 26_27ab Inhibitor Mock

value: miR-27a & miR-27b inhibitor transfected


title: KOIRrna_1


title: Koshamrna_3

value: Normoxia


title: A549 miR-27a shMIMIC clone 1, Mock-infected,rep 3

description: 13_27a clone 1 Mock

source_name: A549 miR-27a clone1

value: A549 miR-27a clone1

value: miR-27a shMIMIC transduced


title: A549 NTC shMIMIC clone 1, Mock-infected rep 2

description: 11_NTC clone 1 Mock

source_name: A549 NTC clone1

value: A549 NTC clone1

value: control shMIMIC transduced


title: A549 NTC shMIMIC clone 1, Mock-infected rep 3

description: 17_NTC clone 1 Mock


title: A549 control mimic transfected, Mock-infected,rep 1

description: 27_CTRL Mimic Mock

value: control mimic transfected


title: A549 miR-27a shMIMIC clone 1, Mock-infected,rep 2

description: 7_27a clone 1 Mock


title: A549 non-targeting control (NTC) shMIMIC clone 1, Mock-infected rep 1

description: 5_NTC clone 1 Mock


title: Koshamrna_1


title: Koshamrna_4


title: Koshamrna_2


title: WTIRrna_4


title: A549 miR-27a shMIMIC clone 1, Mock-infected,rep 1

description: 1_27a clone 1 Mock


title: WTIRrna_3


title: A549 WT, Mock-infected rep 1

description: 6_A549 WT Mock


title: Cp_NecLo_Sta_Rep3

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description:
Cp_NecLo_TPM.csv
Necromass_DEG.xlsx

data_processing:
The raw FASTQ files were quality checked, aligned to existing genomes, and analyzed for differential expression using the Galaxy platform. Unless otherwise noted below, default parameters were in all analysis tools used except in cases where strandedness was specified (all RNAseq data were unstranded). Briefly, RNAseq data were concatenated using the concatenate data sets: tail-to-head (cat) tool. Transcript quality was tested using FastQC, which indicated read trimming was unnecessary for any of the files. Transcripts were next aligned to their respective reference genomes using the HISAT2 tool and quantified using the htseq-count tool. Reference genome files for C. japonicus Ueda107 (ASM1922v1) and C. pinensis DSM2588 (ASM2400v1) were obtained from ENSEMBLE, while that for S. marcescens PIC3611 was retrieved from NCBI Refseq (ASM2260299v1). Due to the differences in reference genome sources, the S. marcescens files required a parameter change in the htseq-count ‘feature type’ from ‘gene’ to ‘exon’. Differential gene expression using DESeq2 compared necromass exponential growth to necromass stationary phase for all three species and glucose for Cp and Sm.
Assembly: C. japonicus Ueda107 (ASM1922v1); C. pinensis DSM2588 (ASM2400v1); S. marcescens PIC3611 (ASM2260299v1)
Supplementary files format and content: TPM for biolgical repliates for a given substrate and bacterial species; DEG with p-values for pair-wise comparisons

organism: Chitinophaga pinensis

source_name: Bacterial cell

extract_protocol:
As per the protocol described in PMID: 22949721
Ribosomal RNA Depletion; RNA Fragmentation and Random Priming; Fist and Second Strand cDNA synthesis; End Repair with 5' phosphorylation and dA-Tailing; Adapter ligation with PCR enrichment; Sequencing

value: Bacterial cell

tag: group

value: NecLo

tag: growth phase

value: Sta


title: KOIRrna_3


title: Cp_NecLo_Sta_Rep2

description:
Cp_NecLo_TPM.csv
Necromass_DEG.xlsx


title: WTIRrna_2


title: Cp_NecLo_Sta_Rep1

description:
Cp_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Wtshamrna_3


title: WTIRrna_1


title: Wtshamrna_4


title: Cp_NecLo_Log_Rep2

description:
Cp_NecLo_TPM.csv
Necromass_DEG.xlsx

value: Log


title: Cp_NecLo_Log_Rep3

description:
Cp_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Cp_NecLo_Log_Rep1

description:
Cp_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Cp_NecHi_Sta_Rep1

description:
Cp_NecHi_TPM.csv
Necromass_DEG.xlsx

value: NecHi


title: Cp_NecHi_Sta_Rep2

description:
Cp_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Wtshamrna_2

value: liver


title: Cp_NecHi_Log_Rep3

description:
Cp_NecHi_TPM.csv
Necromass_DEG.xlsx


title: iris, WT, rep1

first: Zheng

last: Liu

address: No. 7 Jinsui Rd, Guangzhou, People 's Republic of China

institute: Zhongshan Ophthalmic center, Sun Yat-sen University

description:
injury
raw_counts.txt

data_processing:
Sequencing was performed on DNBSEQ with read length of SE50 on BGIseq500 platform (BGI-Shenzhen，China).
Filtered clean reads were aligned to the mouse genome using hierarchical indexing for spliced alignment of transcripts 2 (HISAT2, v2.0.4) and Bowtie2 (v2.2.5).
After removal of rare genes (transcription per million values < 2 in all groups), gene expression comparison differently expressed genes (DEGs, adj p<0.05) were conducted using DESeq2 (v1.4.5) using the following thresholding parameters: fold change>1.5; adjusted p value<0.05 by the Benjamini-Hochberg’s procedure).
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample

source_name: iris

growth_protocol: Vegfr3fl/fl;Prox1CreERT2 mice and littermate VEGFR3fl/fl mice were maintained in-house under the specific pathogen-free (SPF) condition

extract_protocol:
RNA was extracted using the Qiagen RNeasy Lipid Mini Kit. 1 µg of qualified RNA was used for the construction of sequencing library
RNA library for RNA-seq were generated using the Illumina TruSeq mRNA sample preparation kit (Illumina)

treatment_protocol:
Corneal alkali injury and sham control was induced in six-week-old mice with 0.5μl 1 M sodium hydroxide solution or PBS for 60 seconds.
Mice were intraperitoneally injected Tamoxifen (80 mg/kg body weight) on days 13th-17th after corneal alkali injury.

value: iris

value: Alkali Injury


title: iris, VR3ko, rep3

description:
injury+vegfr3 ko
raw_counts.txt

value: Vegfr5 depletion


title: Wtshamrna_1

value: WT


title: iris, WT, rep2

description:
injury
raw_counts.txt


title: iris, WT, rep3

description:
injury
raw_counts.txt


title: Cp_Glc_Sta_Rep3

description:
Cp_Glc_TPM.csv
Necromass_DEG.xlsx

value: Glc


title: Cp_NecHi_Sta_Rep3

description:
Cp_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Cp_NecHi_Log_Rep2

description:
Cp_NecHi_TPM.csv
Necromass_DEG.xlsx


title: iris, ShamControl, rep3

description:
PBS sham
raw_counts.txt

value: PBS


title: Cp_Glc_Sta_Rep2

description:
Cp_Glc_TPM.csv
Necromass_DEG.xlsx


title: iris, VR3ko, rep1

description:
injury+vegfr3 ko
raw_counts.txt

value: Vegfr3 depletion


title: iris, ShamControl, rep2

description:
PBS sham
raw_counts.txt


title: Cp_NecHi_Log_Rep1

description:
Cp_NecHi_TPM.csv
Necromass_DEG.xlsx


title: iris, VR3ko, rep2

description:
injury+vegfr3 ko
raw_counts.txt

value: Vegfr4 depletion


title: Cj_NecLo_Sta_Rep2

description:
Cj_NecLo_TPM.csv
Necromass_DEG.xlsx

organism: Cellvibrio japonicus


title: Cj_NecLo_Log_Rep3

description:
Cj_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecLo_Sta_Rep1

description:
Cj_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecLo_Log_Rep1

description:
Cj_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecLo_Log_Rep2

description:
Cj_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecHi_Sta_Rep3

description:
Cj_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecHi_Sta_Rep2

description:
Cj_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecHi_Sta_Rep1

description:
Cj_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Cp_Glc_Sta_Rep1

description:
Cp_Glc_TPM.csv
Necromass_DEG.xlsx


title: Cp_Glc_Log_Rep2

description:
Cp_Glc_TPM.csv
Necromass_DEG.xlsx


title: Cp_Glc_Log_Rep3

description:
Cp_Glc_TPM.csv
Necromass_DEG.xlsx


title: Cj_NecLo_Sta_Rep3

description:
Cj_NecLo_TPM.csv
Necromass_DEG.xlsx


title: iris, ShamControl, rep1

description:
PBS sham
raw_counts.txt


title: Cj_NecHi_Log_Rep3

description:
Cj_NecHi_TPM.csv
Necromass_DEG.xlsx


title: 9pool-AS, scRNAseq + CITE-seq

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

institute: Weill Cornell Medicine

description: 10x Genomics

data_processing:
Cellranger Single-Cell Software Suite (version 6.1.2) was used to perform sample de-multiplexing, barcode processing, and single-cell 5’ and V(D)J counting, and Cellranger mkfastq was used to de-multiplex raw base call (BCL) files into sample-specific fastq files. Subsequently, reads were aligned to the GRCh38 human genome. Cellranger counts and Cellranger vdj package within the Cellranger pipeline were used to identify gene expression and assemble V(D)J pairs of antibodies.
Assembly: GRCh38-2020-A
Supplementary files format and content: compressed tar.gz file, has barcodes.tsv, genes.tsv, matrix.mtx 3 files, which are outputs from CellRanger pipeline

source_name: Blood Cells

extract_protocol:
Chromium next GEM single cell 5' HT v2 protocol
The libraries were constructed based on the 10X Genomics protocols for  5’ gene expression, BCR V(D)J and cell surface protein mapping library construction.
Libraries were sequenced using an Illumina NextSeq1000 at the Weill Cornell Medicine.

value: Blood Cells


title: 8pool-CA, scRNAseq + CITE-seq

description: 10x Genomics


title: Cj_NecHi_Log_Rep2

description:
Cj_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Primary T cells 4 PTC IP

source_name: Primary T cells

value: Primary T cells

value: PTC

value: m6A-binding RNA


title: S414, scRNAseq + CITE-seq

description: 10x Genomics


title: 9pool-CA, scRNAseq + CITE-seq

description: 10x Genomics


title: Cj_NecHi_Log_Rep1

description:
Cj_NecHi_TPM.csv
Necromass_DEG.xlsx

value: Bacterial cell


title: hUCB_healthy donor5

city: Palma

first: Josep

last: Muncunill Farreny

address: Carretera de Valldemossa, 79. Hospital Universitario Son Espases

country: Spain

institute: IdISBa

hyb_protocol: Samples were hybridized with GeneChip Human Clariom D Arrays (Affymetrix, Thermo Fisher Scientific) and scanned at the IdISBa Genomic Core Facility.

scan_protocol: Array scanning was performed by using the GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix, Thermo Fisher Scientific).

data_processing: Preprocessing was performed in R/Bioconductor using the oligo package. Raw CEL files were summarized and normalized through RMA (Robust Multichip Average) and quantile normalization (oligo::rma). Quality control analyses were performed with arrayQualityMetrics package. Probes were annotated with packages pd.clariom.s.human, clariomshumantranscriptcluster.db and annotation file from Affymetrix (Clariom S Array, human Transcript Cluster Annotations, CSV, Release 36).

label: biotin

source_name: umbilical cord blood cells from heathy donor

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the GeneChip WT Plus Reagent Kit (Affymetrix, Thermo Fisher Scientific) and then fragmented and biotin-labeled with the WT Terminal Labeling Kit (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Cells were grown in flasks coated with rat tail collagen type I high concentration and cultured in EGM-2 Endothelial Cell Growth Medium-2 BulletKit (CC-3162).

extract_protocol: Total RNA was extracted using QIAzol Lysis Reagent from miRNeasy Mini Kit following the manufacturer's protocol.

treatment_protocol: During pregnancy, fetus was exposed to OSA conditions caused by OSA-affected mother.

value: human umbilical cord blood cells

tag: developmental stage

value: Newborn

tag: disease state

value: Healthy